Thermo Scientific Applied Biosystems ProFlex PCR System User manual

ProFlex™PCR System Installation and Operation
Catalog Numbers 4483636, 4483637, 4483638, 4484071, 4484073, 4484074, 4484075, 4484076, 4484078
Pub. No. 4483807 Rev. G
Note: For safety and biohazard guidelines, see the “Safety”
appendix in the ProFlex™PCR System User Guide (Pub. No.
MAN0007697). Read the Safety Data Sheets (SDSs) and follow
the handling instructions. Wear appropriate protective eyewear,
clothing, and gloves.
Product description
This document summarizes procedures for installing and using
the ProFlex™Thermal Cycler, with "better than gradient™" VeriFlex™
technology. For detailed instructions, see the ProFlex™PCR
System User Guide (Pub. No. MAN0007697).
Figure 1 ProFlex™3 × 32‑Well PCR System
Required materials not provided
• Can of compressed air (For use in cleaning wells of sample
block).
•(Optional) Electrical protective devices.
Note: The use of one or more of the following electrical
protective devices is recommended.
·Power line regulator (1.5 kVA)
·Surge protector/line conditioner (10-kVA)
·Uninterruptible power supply (1.5-kVA)
Set up the ProFlex™Thermal Cycler
IMPORTANT! Save the packing materials and box in case you
need to ship the instrument in for service.
1. Open the shipping crate to unpack the ProFlex™Thermal
Cycler. The instrument is contained in three boxes; one with
the base module, a second with the sample block, and the
third containing accessories.
2. Remove the packaging material, then inspect the instrument
for shipping damage.
Figure 2 ProFlex™Base module packaging
Figure 3 ProFlex™3x32-Well Sample Block and
accessories packaging
3. Use compressed air to clear out each well of the sample
block to remove particles that may have collected inside
during shipping.
4. Place the instrument at an installation site that:
• Meets the spatial and weight requirements for the
thermal cycler (see “Technical specifications” on
page 7).
• Is within 1 m (3 ft) of a 800-VA power receptacle.
QUICK REFERENCE
For Research Use Only. Not for use in diagnostic procedures.

5. Turn the base module to view the rear of the instrument.
Figure 4 Rear view of ProFlex™Base and ProFlex™3x32-
Well Sample Block
6. Place the block (ProFlex™96-Well Sample Block or ProFlex™
3x32-Well Sample Block) on top of the ProFlex™Base
module with the latching mechanism positioned to the right
hand side.
Figure 5 Latching mechanism during installation
7. Push the latching mechanism all the way to the left to secure
the block onto the base.
Figure 6 Latching mechanism securing the ProFlex™
3x32-Well Sample Block to the ProFlex™Base module
8. Connect the instrument to a power outlet.
a. Connect the power cord to the instrument.
1Power cord port
b. Install any desired electrical protective devices.
c. Connect the power cord to an 800-VA power
receptacle.
9. Connect the PCR instrument to the Internet.
• Connect through the instrument Ethernet port using a
cable.
• Connect via wireless connection with the USB-enabled
Wi-Fi Module (Cat. No. A26774).
Insert the Wi-Fi Module into the USB port at the back of
the instrument. For instructions on setting up the wireless
connection, see “How to set up the wireless connection for
the ProFlex™Thermal Cycler” on page 3.
1USB WiFi port
2Ethernet port
10. Press the power button, then wait for the instrument to
start up. Proceed with the installation after the touchscreen
displays the Home screen, indicating that the instrument is
active.
When you power on the instrument, the instrument may
require about 30 seconds to start up.
1Power switch
The Home screen is displayed upon successful installation.
Figure 7 ProFlex™3x32-Well System Home screen
Note: The image shows the Home screen for the ProFlex™
3x32-Well System. In the ProFlex™96-Well System, the
ProFlex™Dual 96-Well System, and the ProFlex™Dual Flat
PCR System, the Home screen displays only one status dial.
2ProFlex™PCR System Installation and Operation Quick Reference

How to set up the wireless connection for the
ProFlex™Thermal Cycler
See “Set up the ProFlex™Thermal Cycler” on page 1 for details on
the USB Wi-Fi Module.
1. Press (Settings) > . Instrument Settings > Network
Connection.
2. In the Network Connection screen, press Wireless.
Once a wireless connection is detected, a list of available
networks is displayed in the Choose Network screen.
3. Press the name of the desired network, then enter the
appropriate credentials to join the network.
4. (Optional) Press Join Other Network to enter a network
manually.
a. Enter the name and security type of the network.
Note: Contact your IT system administrator for
information on security type.
You can select from the following options:
• WEP
• WPA Personal
• WPA2 Personal
• WPA Enterprise
• WPA2 Enterprise
b. Press Join, then enter the appropriate credentials to
join the network.
Upon successful authentication, the instrument is linked to
the network.
Set up mobile and cloud connectivity to the
ProFlex™Thermal Cycler and your mobile device
Create a user profile on the PCR instrument
1. Select (Sign In) > Get started.
2. Fill in the required text fields and enter a four digit PIN to
create your user profile.
Note: The first profile created is automatically given an
Administrator profile (indicated by an asterisk after the
Username).
Create a Connect account
1. Go to thermofisher.com/connect from your web browser.
2. Click Sign up now and follow the prompts to create an
account.
Link the PCR instrument to Connect (Administrator only)
The procedure to link the Administrator profile to Connect only
needs to be performed the first time the PCR instrument is added
to Connect.
1. Press (Sign In) > Sign In, then select the Administrator
profile.
2. Log in. (The default password for the Administrator profile is
"password<last four digits of instrument serial number>").
You will then be redirected back to the home screen.
3. Press (Settings) > Instrument Settings > Remote
Service.
4. Set Remote Service to "On", then press OK.
5. Press (My Profile) on the home screen.
6. Select Cloud, then enter the Connect login and password
associated with the Administrator profile.
7. Press Link Account.
Upon successful authentication, the Administrator profile is
linked to Connect.
Note: If an instrument is already linked to Connect, you will
have the option to unlink the instrument if desired.
Connect by PC
Note: Multiple instruments can be added to your Connect
account, but only one user profile from each instrument can be
linked to your account.
1. Press (Sign In) > Sign In, then select your user profile.
2. Log in to your user profile.
You will then be redirected back to the home screen.
3. Press (Settings) > Instrument Settings > Remote
Service.
4. Set Remote Service to "On", then press OK.
5. Press (My Profile) on the home screen.
6. Select Cloud, then enter your Connect account login and
password.
7. Press Link Account.
Upon successful authentication, the the user profile is linked
to Connect.
ProFlex™PCR System Installation and Operation Quick Reference 3

Connect by mobile device
1. Download the "Instrument Connect Mobile Application" on
your mobile device.
a. For iPad™or iPhone™devices, download the
application from the iTunes™music store by searching
for Instrument Connect by Thermo Fisher Scientific.
b. For Android devices, download the application from
Google™Play by searching for Instrument Connect by
Thermo Fisher Scientific.
2. Launch the Instrument Connect Mobile Application and log
in using your Connect login and password.
3. Capture the QR code on the instrument screen.
How to use the ProFlex™Thermal Cycler
Operate the ProFlex™Thermal Cycler using the touchscreen. For
detailed instructions on using the instrument, refer to the ProFlex™
PCR System User Guide (Pub. No. MAN0007697), available at
thermofisher.com/proflex
From the instrument Home screen, you can set up and run a new
Method using the following instructions:
1. Press New Method or Set Up Run on the status dial of an
available block.
2. Select a Method template.
3. Edit the parameters of the template such as temperature,
time, number of steps/stages.
4. For advanced editing options, press Manage Steps >
Advanced Options. Advanced editing options include:
VeriFlex™for optimization, simulation modes, ramp rates,
and AutoDelta.
5. Save the new Method to a folder or directly start a run by
pressing Start Run.
Note: For the ProFlex™3x32 Well PCR System, you will need
to choose a block prior to starting a run.
Maintenance guidelines
CAUTION! During instrument operation, the temperature
of the heated cover can be as high as 110°C, and the
temperature of the sample block(s) can be as high as
100°C. Before performing the procedure, keep hands away
until the heated cover and sample block(s) reach room
temperature.
To ensure proper operation:
• Regularly:
– Wipe the instrument surfaces with a lint-free cloth.
– Clean the vents, touchscreen, and sample block of the
instrument.
– Clean the sample wells with 100% isopropanol.
• Use only consumables recommended by Thermo Fisher
Scientific for the instrument.
Use of consumables that are larger or smaller than the
specified volume can damage the instrument, contaminate
the sample block, and/or decrease the PCR yield (due to
inecient thermal transfer).
•Do not use sharp objects on the touchscreen.
Use only your fingers or blunt objects to enter commands
on the instrument touchscreen. Sharp and/or pointed objects
such as writing utensils can damage the surface of the
touchscreen.
•Back up frequently.
Routinely back up the configurations and files on your
instrument to a USB drive. Regular backups protect against
data loss caused by user error, power failure, or instrument
error. For more information, see the ProFlex™PCR System
User Guide (Pub. No. MAN0007697).
How to use the MicroAmp™3 × 32-Well Retainer
IMPORTANT! The retainer is essential for optimal performance,
and its usage is recommended at all times for the ProFlex™
3 × 32‑Well PCR System. The retainer allows pressure to be
distributed evenly over the tubes to ensure a proper seal, and
prevent tubes from being crushed or deformed.
The retainer is compatible for use with MicroAmp™tubes and tube
strips.
Figure 8 MicroAmp™3x32-Well Retainer
4ProFlex™PCR System Installation and Operation Quick Reference

Prepare samples using MicroAmp™Reaction Tubes or
Tube Strips
1. Pipette the reaction mixture into the reaction tubes.
2. Cap the tubes, or seal the tube strips with cap strips using
the Cap Installing Tool.
3. Ensure a MicroAmp™3 × 32-Well Retainer is on the sample
block(s) to be used.
4. Load the tubes or tube strips into the sample block(s).
How to use the MicroAmp™96-well Tray and
Retainer
IMPORTANT! Use the MicroAmp™96-well Tray and Retainer to
prevent crushing of tubes in the thermal cycler.
When small number of tubes (1–2 tube strips or ≤8–16 tubes are
placed in the sample block without support, they can be crushed
or deformed when the lid of the thermal cycler is closed over the
block. Using the tray and retainer set allows the pressure to be
distributed evenly over the tubes and prevents uneven pressure
across the block.
Using the tray and retainer set is optional when using ≥3 tube
strips or ≥16 tubes that are distributed evenly across the block.
• The blue tray and retainer set is compatible for use with
MicroAmp™single tubes or tube strips with separate cap
strips.
• The blue tray by itself is compatible for use with MicroAmp™
tube strips with attached caps.
• The black retainer is compatible for use with single
MicroAmp™reaction tubes with attached caps.
Prepare samples using MicroAmp™tubes/tube strips
with separate cap strips
1. Separate the blue tray and retainer by squeezing the release
catch as indicated in the graphic.
1
2
3
1
1Release catch
2MicroAmp™96-Well Retainer
3MicroAmp™96-Well Tray
2. Place the blue tray on the 96-well base.
3. Load the tube strips on the tray.
4. Pipette the reaction mixture into the tubes.
5. Place the blue retainer over the tubes and snap the retainer
into the tray.
6. Seal the tube strip using a MicroAmp™cap strip. See “Seal
tubes strips with cap strips” on page 6 for instructions.
7. Remove the blue tray/retainer assembly containing the
sealed tube strips from the 96-well base and place the
assembly into the instrument.
1
2
4
3
5
1MicroAmp™8-Cap strip
2MicroAmp™96-Well Retainer
3MicroAmp™8-Tube Strip (0.2-mL) or MicroAmp™Reaction
Tube without Cap (0.2-mL)
4MicroAmp™96-Well Tray
5MicroAmp™Splash Free 96-Well Base
ProFlex™PCR System Installation and Operation Quick Reference 5

Prepare samples using MicroAmp™tube strips with
attached caps
1. Separate the blue tray and retainer by squeezing the release
catch as indicated in the graphic.
1
2
3
1
1Release catch
2MicroAmp™96-Well Retainer
3MicroAmp™96-Well Tray
2. Place the blue tray on the 96-well base.
3. Load the tube strips on the tray.
4. Pipette the reaction mixture into the tubes.
5. Seal the tube strip using a MicroAmp™cap strip. See “Seal
tubes strips with cap strips” on page 6 for instructions.
6. Remove the blue tray containing the sealed tube strips from
the 96-well base and place the tray and sealed tube strips
into the instrument.
1MicroAmp™8-Tube Strip with Attached Caps (0.2-mL)
2MicroAmp™96-Well Tray
3MicroAmp™Splash Free 96-Well Base
Seal tubes strips with cap strips
IMPORTANT! Apply significant downward pressure on the
sealing tool in all steps to form a complete seal on top of the
tubes.
1. Align and place the cap strips on the tubes.
2. Seal the cap strips using the rocking capping tool:
a. Slip your fingers through the handle with the holes in
the tool facing down.
b. Place the holes in the tool over the first eight caps in a
row.
c. Rock the tool back and forth a few times to seal the
caps.
d. Repeat for remaining caps in the row, then for all
remaining rows.
Prepare samples using MicroAmp™Reaction Tubes
1. Set the black tray on a 96-well base.
2. Place the reaction tubes in the black tray.
1
2
3
1MicroAmp™Reaction Tube with Cap (0.2-mL)
2MicroAmp™96-Well Tray for VeriFlex™Blocks
3MicroAmp™Splash Free 96-Well Base
3. Pipette the reaction mixture into the reaction tubes.
4. Cap the tubes.
5. Remove the black tray with sealed reaction tubes from the
96-well base and place the tray and sealed tubes into the
instrument.
6ProFlex™PCR System Installation and Operation Quick Reference

Technical specifications
The following table displays the system specifications for an instrument using the ProFlex™96-Well Sample Block, ProFlex™3x 32-Well
Sample Block, ProFlex™2x 96-Well Sample Block, ProFlex™2x Flat Sample Block, ProFlex™2x 384-Well Sample Block
Table 1 ProFlex™Thermal Cycler technical specifications: ProFlex™96-Well Sample Block, ProFlex™3x32-Well Sample Block,
ProFlex™2x 96-Well Sample Block, ProFlex™2x Flat Sample Block, ProFlex™2x 384-Well Sample Block
Specification
Block format
3 x 32-well, 0.2 mL
(Cat. No. 4483638)
96-well, 0.2 mL
(Cat. No. 4483637)
2 x 96-
well, 0.2 mL
(Cat. No. 4484071)
2 x Flat block
(Cat. No. 4484074)
2 x 384-well, 0.2 mL
(Cat. No. 4484072)
Maximum block ramp rate 6.0°C/sec 3.0°C/sec 1.6°C/sec 3.0°C/sec
Maximum sample ramp rate 4.4°C/sec 1.6°C/sec N/A 1.6°C/sec
Temperature accuracy ±0.25°C (35°C to 99.9°C)
Temperature range 0°C to 100.0°C
Temperature uniformity <0.5°C (20 seconds after reaching 95°C)
Dimensions • Height: 27.2 cm (10.7 in)
• Width: 33.0 cm (13 in)
• Depth: 56.5 cm (22 in)
Weight 18.8 kg (41 lb) 20.4 kg (45 lb)
PCR volume range 10–80 µL 10–100 µL 33 nL 5–20 µL
Instrument memory USB, onboard
Display interface 8.4-inch color TFT LCD
Power 100–240 V, 50–60 Hz Max: 950 VA
Note: For Australia (AU) / New Zealand (NZ) only: 230 VAC, 50 Hz, Max: 950 W, Max Current: 10 A
VeriFlex™blocks independent control
2 temperature zones
per block
(5°C zone-to-zone)
6 temperature zones
25°C (5°C zone-to-
zone),
N/A
Ambient humidity 15% - 80% Relative Humidity, non-condensing (acceptable range)
Ambient operating
temperature 15°C to 30°C (acceptable range)
Table 2
Port Description
AC power cable port
10/100 Fast Ethernet port for connecting to a network
USB v1.0 port for connecting to an external network drive, jump drive, or other USB storage device
RS232 serial communication port for connecting the probe for the Temperature Verification Kit
USB v1.0 port for connecting to USB-enabled Wi-Fi Card
ProFlex™PCR System Installation and Operation Quick Reference 7

Accessory products
Product Cat. No.
96-well 0.2-mL reaction plates
MicroAmp™Optical 96-Well Reaction Plate N8010560, 4316813
MicroAmp™Optical 96‑Well Reaction Plate with Barcode 4306737, 4326659
MicroAmp™Optical 96-Well Reaction Plate with Barcode & Optical Caps 403012
MicroAmp™Optical 96-Well Reaction Plate with Barcode & Optical Adhesive Films 4314320
MicroAmp™EnduraPlate™Optical 96-Well Clear Reaction Plates with Barcode 4483354, 4483352
MicroAmp™TriFlex 3 x 32-Well PCR Reaction Plate A32810, A32811
96-well 0.1-mL reaction plates
MicroAmp™Fast Optical 96-Well Reaction Plate, 0.1 mL 4346907
MicroAmp™Fast Optical 96‑Well Reaction Plate with Barcode, 0.1 mL 4346906, 4366932
MicroAmp™EnduraPlate™Optical 96-Well Fast Clear Reaction Plates with Barcode 4483485, 4483494
384-well reaction plates
MicroAmp™Optical 384-Well Reaction Plate 4343370
MicroAmp™Optical 384-Well Reaction Plate with Barcode 4309849, 4326270, 4343814
MicroAmp™EnduraPlate™Optical 384-Well Clear Reaction Plates with Barcode 4483285, 4483273
Strip tubes and caps
MicroAmp™Fast 8-Tube Strip, 0.1 mL 4358293
MicroAmp™Optical 8-Tube Strip with Attached Optical Caps, 0.2 mL A30588
MicroAmp™Optical 8-Tube Strip with Attached Domed Caps, 0.2 mL A30589
MicroAmp™8-Tube Strip, 0.2 mL N8010580
MicroAmp™Optical 8-Tube Strip, 0.2 mL 4316567
MicroAmp™8-Cap Strip, clear N8010535, N8011535
MicroAmp™Optical 8-Cap Strips 4323032
MicroAmp™12-Cap Strip N8010534, N8011534
Single Tubes
MicroAmp™Fast Reaction Tube with Cap, 0.1 mL 4358297, 4358293
MicroAmp™Reaction Tube with Cap, 0.2 mL N8010540, N8011540, N8010612
MicroAmp™Reaction Tube without Cap, 0.2 mL N8010533, N8011533
MicroAmp™Optical Tube without Cap, 0.2 mL N8010933
Seals and covers
MicroAmp™Clear Adhesive Film 4306311
MicroAmp™Optical Adhesive Film 4360954, 4311971
MicroAmp™32‑Well Clear Adhesive Film A32812
Accessories
MicroAmp™Splash-Free 96-Well Base 4312063
MicroAmp™96-Well Support Base 4379590
MicroAmp™96-Well Base N8010531
MicroAmp™96-Well Reaction Tube/Tray/Retainer Set, 0.2 mL 403083, 403086
8ProFlex™PCR System Installation and Operation Quick Reference

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17 June 2021